File: homGeneMapping.1

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'\" t
.\"     Title: homgenemapping
.\"    Author: [see the "AUTHORS" section]
.\" Generator: Asciidoctor 1.5.5.dev
.\"      Date: 
.\"    Manual: \ \&
.\"    Source: \ \&
.\"  Language: English
.\"
.TH "HOMGENEMAPPING" "1" "" "\ \&" "\ \&"
.ie \n(.g .ds Aq \(aq
.el       .ds Aq '
.ss \n[.ss] 0
.nh
.ad l
.de URL
\\$2 \(laURL: \\$1 \(ra\\$3
..
.if \n[.g] .mso www.tmac
.LINKSTYLE blue R < >
.SH "NAME"
homgenemapping \- create summary of gene homology
.SH "SYNOPSIS"
.sp
\fBhomGeneMapping\fP [options] \-\-gtfs=gffilenames.tbl \-\-halfile=aln.hal
.SH "DESCRIPTION"
.sp
\fBhomGeneMapping\fP takes a set of gene predictions of different genomes and a hal
alignment of the genomes and prints a summary for each gene, e.g.
.sp
.RS 4
.ie n \{\
\h'-04'\(bu\h'+03'\c
.\}
.el \{\
.sp -1
.IP \(bu 2.3
.\}
how many of its exons/introns are in agreement with genes of other genomes
.RE
.sp
.RS 4
.ie n \{\
\h'-04'\(bu\h'+03'\c
.\}
.el \{\
.sp -1
.IP \(bu 2.3
.\}
how many of its exons/introns are supported by extrinsic evidence from any of the genomes
.RE
.sp
.RS 4
.ie n \{\
\h'-04'\(bu\h'+03'\c
.\}
.el \{\
.sp -1
.IP \(bu 2.3
.\}
a list of geneids of homologous genes
.RE
.SH "OPTIONS"
.SS "Mandatory parameters"
.sp
\fB\-\-halfile=aln.hal\fP
.RS 4
input hal file
.RE
.sp
\fB\-\-gtfs=gtffilenames.tbl\fP
.RS 4
a text file containing the locations of the input gene files
and optionally the hints files (both in GTF format).
The file is formatted as follows:
.sp
.if n \{\
.RS 4
.\}
.nf
name_of_genome_1  path/to/genefile/of/genome_1  path/to/hintsfile/of/genome_1
name_of_genome_2  path/to/genefile/of/genome_2  path/to/hintsfile/of/genome_2
\&...
name_of_genome_N  path/to/genefile/of/genome_N  path/to/hintsfile/of/genome_N
.fi
.if n \{\
.RE
.\}
.RE
.SS "Additional options"
.sp
\fB\-\-cpus=N\fP
.RS 4
N is the number of CPUs to use (default: 1)
.RE
.sp
\fB\-\-noDupes\fP
.RS 4
do not map between duplications in hal graph. (default: off)
.RE
.sp
\fB\-\-halLiftover_exec_dir=DIR\fP
.RS 4
Directory that contains the executable halLiftover
If not specified it must be in $PATH environment variable.
.RE
.sp
\fB\-\-tmpdir=DIR\fP
.RS 4
a temporary file directory that stores lifted over files. (default \(aqtmp/\(aq in current directory)
.RE
.sp
\fB\-\-outdir=DIR\fP
.RS 4
file directory that stores output gene files. (default: current directory)
.RE
.sp
\fB\-\-printHomologs=FILE\fP
.RS 4
prints disjunct sets of homologous transcripts to FILE, e.g.
.sp
.if n \{\
.RS 4
.\}
.nf
# 0     dana
# 1     dere
# 2     dgri
# 3     dmel
# 4     dmoj
# 5     dper
(0, jg4139.t1) (0, jg4140.t1) (1, jg7797.t1) (2, jg3247.t1) (4, jg6720.t1) (5, jg313.t1)
(1, jg14269.t1) (3, jg89.t1) (5, jg290.t1)
\&...
Two transcripts are in the same set, if all their exons/introns are homologs and their are
no additional exons/introns.
This option requires the Boost C++ Library
.fi
.if n \{\
.RE
.\}
.RE
.SH "EXAMPLE"
.sp
homGeneMapping \-\-noDupes \-\-halLiftover_exec_dir=~/tools/progressiveCactus/submodules/hal/bin \-\-gtfs=gtffilenames.tbl \-\-halfile=msca.hal
.SH "AUTHORS"
.sp
AUGUSTUS was written by M. Stanke, O. Keller, S. K├Ânig, L. Gerischer and L. Romoth.
.SH "ADDITIONAL DOCUMENTATION"
.sp
An exhaustive documentation can be found in the file /usr/share/augustus/README.TXT.